20-1724191-T-C

Position:

• chr20-1724191-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.514 in 151,994 control chromosomes in the GnomAD database, including 20,586 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (20586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78132 AN: 151876 Hom.: 20560 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.471

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.514 AC: 78200 AN: 151994 Hom.: 20586 Cov.: 32 AF XY: 0.509 AC XY: 37803 AN XY: 74296

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.471

Alfa AF: 0.535 Hom.: 28715

Bravo AF: 0.522

Asia WGS AF: 0.390 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs202516; hg19: chr20-1704837;